If you are one of those people that does not enable WiFi on their 3DS to avoid system updates and prompts, you are going to need to enable it long enough somewhere your 3DS has an internet connection for the update to be downloaded. DO NOT UPDATE FROM THE PROMPT, USE IT ONLY AS AN INDICATION THAT YOU HAVE ALREADY DOWNLOADED THE UPDATE. If you have not been nagged at some point about a new system update your not ready to go, or at the minimum you will have to leave WiFi on in step 9, which may be dangerous but I'm not sure why.
IF YOU GET A PROMPT TO UPDATE AT ANY POINT DURING THESE STEPS DO NOT ACCEPT IT.
1. Back up your 3DS's SD to your computer. If you have not copied the "Launcher.dat" file from the Gatway 2.0 distribution to your SD yet, do so now, overwrite any old Loader.bin files if present
2. Put the SD back in your 3DS
3. Start Gateway mode while holding down the left shoulder button
4. At the menu shift all the way to the right and select "FORMAT EMUNAND", hit start and wait until it finishes (my 8GB SD took around 10 minutes, I think (wasn't really paying attention or watching a clock))
5. At the menu again shift back two icons to "BACK UP SYSTEM NAND" and select it, hit start and wait until it finishes (again around 10 minutes)
6. Power down your 3DS and remove the SD, back up the "NAND.BIN" file that's on it to your computer
7. If the 3DS created a folder on your SD named "Nintendo 3DS" delete it, then put the files back from step 1 on to your SD... DO NOT JUST OVERWRITE THE "NEW" NINTENDO 3DS FOLDER ON THE SD W/ THE OLD BACK UP, DELETE IT FIRST! Make sure the "Launcher.dat" file from the GW 2.0b distro is present in the root of your SD. I left the NAND.BIN file on my SD, but I don't think you need to, the NAND backup GW mode uses is on a partition of it's own, I believe, the file is just there to make it easy for you to back it up
8. Put the SD back in your 3DS
9. Power on and disable WiFi. Removing your connection settings isn't really required, I think GW are just being overly cautious, but if you feel the need to remove your connection settings do it now
10. Enter GW mode (no need to hold the L button)
11. Enter "System Settings" and look for the "GW3D" in front of your system version at the bottom right corner of the top screen. If it's not there restart GW mode (you should be able to do it from here w/o reinstalling the blue cart exploit)
IF YOU DO NOT SEE THE "GW3D" IN FRONT OF YOUR SYSTEM VERSION DO NOT CONTINUE. DO NOT DO ANYTHING ELSE IN THE SYSTEM MENU OR LEAVE IT OR YOU RISK LEAVING GW MODE (this is where most people screw up it seems)
12. Enter "Other Settings", scroll right to the last page and select "System Update"... And then update
ONLY EVER UPDATE VIA STEPS 10 - 12. DO NOT UPDATE FROM A PROMPT FROM THE 3DS'S MAIN MENU OR VIA A GAME CARTRIDGE, EVEN IF YOUR ARE ON EMUNAND.
Does that help, or do we still need a blurry video commentated by the usual YouTube dumb ass?